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Liu TY, Hsu HY, You YS, Hsieh YW, Lin TC, Peng CW, Huang HY, Chang SS, Tsai FJ. Efficacy of Warfarin Therapy Guided by Pharmacogenetics: A Real-world Investigation Among Han Taiwanese. Clin Ther 2023; 45:662-670. [PMID: 37301690 DOI: 10.1016/j.clinthera.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/01/2023] [Accepted: 04/10/2023] [Indexed: 06/12/2023]
Abstract
PURPOSE The anticoagulation activity of warfarin in populations with CYP2C9, VKORC1, and CYP4F2 variants differs between individuals and is correlated with poor international normalized ratio (INR) control. Pharmacogenetics-guided warfarin dosing has been successfully developed for patients with genetic variations in recent years. However, few real-world data have been used to investigate the INR and warfarin dosage and the time to target INR. This study examined the largest collection of genetic and clinical real-world data related to warfarin to provide further evidence supporting the benefits of pharmacogenetics in clinical outcomes. METHODS We retrieved a total of 69,610 INR-warfarin records after the index date from 2,613 patients in the China Medical University Hospital database between January 2003 and December 2019. Each INR reading was obtained from the latest laboratory data after the hospital visit date. Patients with a history of malignant neoplasms or pregnancy before the index date were excluded, as were patients without data on INR measurements after the fifth day of prescription, genetic information, or gender variables. The primary outcomes were the INR and warfarin dosage during days 7, 14, 28, 56, and 84 after prescription. The secondary outcome was the time required to reach the INR ranges of 1.5 to 3.0 and >4.0. FINDINGS A total of 59,643 INR-warfarin records from 2188 patients were retrieved. The average INR was higher for homozygous carriers of the minor allele at CYP2C9 and VKORC1 during the first 7 days (1.83 [1.03] [CYP2C9*1] and 2.46 [1.44] [CYP2C9*3], P < 0.001; 1.39 [0.36] [rs9923231 G/G], 1.55 [0.79] [rs9923231 G/A], and 1.96 [1.13] [rs9923231 A/A], P < 0.001) than for the wild-type allele. These patients with variants required lower warfarin doses than those with the wild-type allele during the first 28 days. CYP4F2 variant patients seemed to require higher doses of warfarin than those in the wild-type group; however, no significant difference in the average INR was observed (1.95 [1.14] [homozygous V433 carriers], 1.78 [0.98] [heterozygous V433M carriers], and 1.66 [0.91] [homozygous M433 carriers], P = 0.016). IMPLICATIONS Our study indicates that genetic variants in the Han population may enhance warfarin responsiveness, which holds clinical relevance. An increased warfarin dosage was not linked to a shorter time to therapeutic INR between CYP4F2 variant patients and those with a wild-type allele. Assessing CYP2C9 and VKORC1 genetic polymorphisms before initiating warfarin treatment in real-world practice is essential for potentially vulnerable patients and is likely to optimize therapeutic dosing.
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Affiliation(s)
- Ting-Yuan Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
| | - Hsing-Yu Hsu
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Ying-Shu You
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
| | - Yow-Wen Hsieh
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Tzu-Ching Lin
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Chun-Wei Peng
- Artificial Intelligence and Data Science, National Chung Hsing University, Taichung, Taiwan.
| | - Hsin-Yi Huang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, Taiwan.
| | - Shih-Sheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan.
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Division of Pediatric Genetics, Children's Hospital of China Medical University, Taichung, Taiwan; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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2
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Steiner HE, Carrion KC, Giles JB, Lima AR, Yee K, Sun X, Cavallari LH, Perera MA, Duconge J, Karnes JH. Local Ancestry-Informed Candidate Pathway Analysis of Warfarin Stable Dose in Latino Populations. Clin Pharmacol Ther 2023; 113:680-691. [PMID: 36321873 PMCID: PMC9957812 DOI: 10.1002/cpt.2787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
Accuracy of warfarin dose prediction algorithms may be improved by including data from diverse populations in genetic studies of dose variability. Here, we surveyed single nucleotide polymorphisms in vitamin K-related genetic pathways for association with warfarin dose requirements in two admixed Latino populations in standard-principal component adjusted and contemporary-local ancestry adjusted regression models. A total of five variants from vitamin K-related genes/pathways were associated with warfarin dose in both cohorts (P < 0.0125) in standard models. Local ancestry-adjusted analysis unveiled 35 associated variants with absolute effects ranging from β = 9.04 ( ±2.23) to 39.18 ( ±10.89) per ancestral allele in the discovery cohort and β = 6.47 (± 2.02) to 17.82 (± 6.83) in the replication cohort. Importantly, we demonstrate the technical validity of the Tractor model in cohorts with admixed ancestry from three founder populations and bring attention to the technical hurdles obstructing the inclusion of diverse, especially admixed, populations in pharmacogenomic research.
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Affiliation(s)
- Heidi E Steiner
- Data Science Institute, University of Arizona, Tucson, Arizona, USA
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, Arizona, USA
| | - Kelvin Carrasquillo Carrion
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Jason B Giles
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, Arizona, USA
| | - Abiel Roche Lima
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Kevin Yee
- Banner University Medical Center-Tucson, Tucson, Arizona, USA
| | - Xiaoxiao Sun
- Department of Biostatistics, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, Arizona, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Minoli A Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jorge Duconge
- Department of Pharmaceutical Sciences, University of Puerto Rico School of Pharmacy, Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, Arizona, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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3
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Abd Alridha A, Al-Gburi K, Abbood S. Warfarin therapy and pharmacogenetics: A narrative review of regional and Iraqi studies. MEDICAL JOURNAL OF BABYLON 2022. [DOI: 10.4103/mjbl.mjbl_70_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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4
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Steiner HE, Giles JB, Patterson HK, Feng J, El Rouby N, Claudio K, Marcatto LR, Tavares LC, Galvez JM, Calderon-Ospina CA, Sun X, Hutz MH, Scott SA, Cavallari LH, Fonseca-Mendoza DJ, Duconge J, Botton MR, Santos PCJL, Karnes JH. Machine Learning for Prediction of Stable Warfarin Dose in US Latinos and Latin Americans. Front Pharmacol 2021; 12:749786. [PMID: 34776967 PMCID: PMC8585774 DOI: 10.3389/fphar.2021.749786] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022] Open
Abstract
Populations used to create warfarin dose prediction algorithms largely lacked participants reporting Hispanic or Latino ethnicity. While previous research suggests nonlinear modeling improves warfarin dose prediction, this research has mainly focused on populations with primarily European ancestry. We compare the accuracy of stable warfarin dose prediction using linear and nonlinear machine learning models in a large cohort enriched for US Latinos and Latin Americans (ULLA). Each model was tested using the same variables as published by the International Warfarin Pharmacogenetics Consortium (IWPC) and using an expanded set of variables including ethnicity and warfarin indication. We utilized a multiple linear regression model and three nonlinear regression models: Bayesian Additive Regression Trees, Multivariate Adaptive Regression Splines, and Support Vector Regression. We compared each model’s ability to predict stable warfarin dose within 20% of actual stable dose, confirming trained models in a 30% testing dataset with 100 rounds of resampling. In all patients (n = 7,030), inclusion of additional predictor variables led to a small but significant improvement in prediction of dose relative to the IWPC algorithm (47.8 versus 46.7% in IWPC, p = 1.43 × 10−15). Nonlinear models using IWPC variables did not significantly improve prediction of dose over the linear IWPC algorithm. In ULLA patients alone (n = 1,734), IWPC performed similarly to all other linear and nonlinear pharmacogenetic algorithms. Our results reinforce the validity of IWPC in a large, ethnically diverse population and suggest that additional variables that capture warfarin dose variability may improve warfarin dose prediction algorithms.
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Affiliation(s)
- Heidi E Steiner
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ, United States
| | - Jason B Giles
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ, United States
| | - Hayley Knight Patterson
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ, United States
| | - Jianglin Feng
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ, United States
| | - Nihal El Rouby
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, FL, United States
| | - Karla Claudio
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, FL, United States.,Department of Pharmaceutical Sciences, University of Puerto Rico School of Pharmacy, Medical Sciences Campus, San Juan, PR, United States
| | - Leiliane Rodrigues Marcatto
- Instituto do Coracao do Hospital das Clinicas da Faculdade de Medicina, HCFMUSP, University of São Paulo, São Paulo, Brazil
| | - Leticia Camargo Tavares
- Instituto do Coracao do Hospital das Clinicas da Faculdade de Medicina, HCFMUSP, University of São Paulo, São Paulo, Brazil.,Faculty of Science, School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Jubby Marcela Galvez
- Center for Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Carlos-Alberto Calderon-Ospina
- Center for Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Xiaoxiao Sun
- Department of Epidemiology Biostatistics, University of Arizona College of Public Health, Tucson, AZ, United States
| | - Mara H Hutz
- Departament of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Stuart A Scott
- Department of Pathology, Stanford University, Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA, United States
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, FL, United States
| | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Jorge Duconge
- Department of Pharmaceutical Sciences, University of Puerto Rico School of Pharmacy, Medical Sciences Campus, San Juan, PR, United States
| | - Mariana Rodrigues Botton
- Departament of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Cells, Tissues and Genes Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Paulo Caleb Junior Lima Santos
- Instituto do Coracao do Hospital das Clinicas da Faculdade de Medicina, HCFMUSP, University of São Paulo, São Paulo, Brazil.,Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-Unifesp, São Paulo, Brazil
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ, United States.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
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Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
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Functional Assessment of 12 Rare Allelic CYP2C9 Variants Identified in a Population of 4773 Japanese Individuals. J Pers Med 2021; 11:jpm11020094. [PMID: 33540768 PMCID: PMC7912942 DOI: 10.3390/jpm11020094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) is an important drug-metabolizing enzyme that contributes to the metabolism of approximately 15% of clinically used drugs, including warfarin, which is known for its narrow therapeutic window. Interindividual differences in CYP2C9 enzymatic activity caused by CYP2C9 genetic polymorphisms lead to inconsistent treatment responses in patients. Thus, in this study, we characterized the functional differences in CYP2C9 wild-type (CYP2C9.1), CYP2C9.2, CYP2C9.3, and 12 rare novel variants identified in 4773 Japanese individuals. These CYP2C9 variants were heterologously expressed in 293FT cells, and the kinetic parameters (Km, kcat, Vmax, catalytic efficiency, and CLint) of (S)-warfarin 7-hydroxylation and tolbutamide 4-hydroxylation were estimated. From this analysis, almost all novel CYP2C9 variants showed significantly reduced or null enzymatic activity compared with that of the CYP2C9 wild-type. A strong correlation was found in catalytic efficiencies between (S)-warfarin 7-hydroxylation and tolbutamide 4-hydroxylation among all studied CYP2C9 variants. The causes of the observed perturbation in enzyme activity were evaluated by three-dimensional structural modeling. Our findings could clarify a part of discrepancies among genotype–phenotype associations based on the novel CYP2C9 rare allelic variants and could, therefore, improve personalized medicine, including the selection of the appropriate warfarin dose.
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7
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Insight on the Genetics of Atrial Fibrillation in Puerto Rican Hispanics. Stroke Res Treat 2021; 2021:8819896. [PMID: 33505650 PMCID: PMC7810540 DOI: 10.1155/2021/8819896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
Non-Hispanic whites present with higher atrial fibrillation (AF) prevalence than other racial minorities living in the mainland USA. In two hospital-based studies, Puerto Rican Hispanics had a lower prevalence of atrial fibrillation of 2.5% than non-Hispanic Whites with 5.7%. This data is particularly controversial because Hispanics possess a higher prevalence of traditional risk factors for developing AF yet have a lower AF prevalence. This phenomenon is known as the atrial fibrillation paradox. Despite recent advancements in understanding AF, its pathogenesis remains unclear. In this study, we compared a genetic dataset of Puerto Rican Hispanics to 111 SNP known to be associated with AF in a large European cohort and determine if they are associated with AF susceptibility in our cohort. To achieve this aim, we performed a secondary analysis of existing data using the following two studies: (1) The Pharmacogenetics of Warfarin in Puerto Ricans study and the (2) A Genomic Approach for Clopidogrel in Caribbean Hispanics, and assess for the presence of European SNPs associated with AF from the genome-wide association study of 1 million people identifies 111 loci for atrial fibrillation. We used data from 555 cardiovascular Puerto Rican Hispanic patients, consisting of 486 control and 69 cases. We found that the following SNPs showed significant association with AF in PHR: rs2834618, rs6462079, rs7508, rs2040862, and rs10458660. Some of these SNPs are proteins involved in lysosomal activities responsible for breaking ceramides to sphingosines and collagen deposition around atrial cardiomyocytes. Furthermore, we performed a machine learning analysis and determined that Native American admixture and heart failure were strongly predictive of AF in PHR. For the first time, this study provides some genetic insight into AF's mechanisms in a Puerto Rican Hispanic cohort.
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8
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Balanovska EV, Petrushenko VS, Koshel SM, Pocheshkhova EA, Chernevskiy DK, Mirzaev KB, Abdullaev S, Balanovsky OP. Cartographic atlas of frequency variation for 45 pharmacogenetic markers in populations of Russia and its neighbor states. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lack of information about the frequency of pharmacogenetic markers in Russia impedes the adoption of personalized treatment algorithms originally developed for West European populations. The aim of this paper was to study the distribution of some clinically significant pharmacogenetic markers across Russia. A total of 45 pharmacogenetic markers were selected from a few population genetic datasets, including ADME, drug target and hemostasis-controlling genes. The total number of donors genotyped for these markers was 2,197. The frequencies of these markers were determined for 50 different populations, comprised of 137 ethnic and subethnic groups. A comprehensive pharmacogenetic atlas was created, i.e. a systematic collection of gene geographic maps of frequency variation for 45 pharmacogenetic DNA markers in Russia and its neighbor states. The maps revealed 3 patterns of geographic variation. Clinal variation (a gradient change in frequency along the East-West axis) is observed in the pharmacogenetic markers that follow the main pattern of variation for North Eurasia (13% of the maps). Uniform distribution singles out a group of markers that occur at average frequency in most Russian regions (27% of the maps). Focal variation is observed in the markers that are specific to a certain group of populations and are absent in other regions (60% of the maps). The atlas reveals that the average frequency of the marker and its frequency in individual populations do not indicate the type of its distribution in Russia: a gene geographic map is needed to uncover the pattern of its variation.
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Affiliation(s)
- EV Balanovska
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia
| | - VS Petrushenko
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
| | - SM Koshel
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - EA Pocheshkhova
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Kuban State Medical Institute, Krasnodar, Russia
| | - DK Chernevskiy
- Bochkov Research Center for Medical Genetics, Moscow, Russia
| | - KB Mirzaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - ShP Abdullaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - OP Balanovsky
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
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El Rouby N, Rodrigues Marcatto L, Claudio K, Camargo Tavares L, Steiner H, Botton MR, Lubitz SA, Fallon EN, Yee K, Kaye J, Scott SA, Karnes J, Caleb Junior de Lima Santos P, Duconge J, Cavallari LH. Multi-site Investigation of Genetic Determinants of Warfarin Dose Variability in Latinos. Clin Transl Sci 2020; 14:268-276. [PMID: 32860733 PMCID: PMC7877858 DOI: 10.1111/cts.12854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/16/2020] [Indexed: 11/28/2022] Open
Abstract
We conducted a multi‐site investigation of genetic determinants of warfarin dose variability in Latinos from the U.S. and Brazil. Patients from four institutions in the United States (n = 411) and Brazil (n = 663) were genotyped for VKORC1 c.‐1639G> A, common CYP2C9 variants, CYP4F2*3, and NQO1*2. Multiple regression analysis was used in the U.S. cohort to test the association between warfarin dose and genotype, adjusting for clinical factors, with further testing in an independent cohort of Brazilians. In the U.S. cohort, VKORC1 and CYP2C9 variants were associated with lower warfarin dose (β = −0.29, P < 2.0 × 10−16; β = −0.21, P = 4.7 × 10−7, respectively) whereas CYP4F2 and NQO1 variants were associated with higher dose (β = 0.10, P = 2 × 10−4; β = 0.10, P = 0.01, respectively). Associations with VKORC1 (β = −0.14, P = 2.0 × 10−16), CYP2C9 (β = −0.07, P = 5.6 × 10−10), and CYP4F2 (β = 0.03, P = 3 × 10−3), but not NQO1*2 (β = 0.01, P = 0.30), were replicated in the Brazilians, explaining 43–46% of warfarin dose variability among the cohorts from the U.S. and Brazil, respectively. We identified genetic associations with warfarin dose requirements in the largest cohort of ancestrally diverse, warfarin‐treated Latinos from the United States and Brazil to date. We confirmed the association of variants in VKORC1, CYP2C9, and CYP4F2 with warfarin dose in Latinos from the United States and Brazil.
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Affiliation(s)
- Nihal El Rouby
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA.,Department of Pharmacy Practice and Administrative Sciences, University of Cincinnati James L. Winkle College of Pharmacy, Cincinnati, Ohio, USA
| | - Leiliane Rodrigues Marcatto
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Karla Claudio
- University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Letícia Camargo Tavares
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Heidi Steiner
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona, USA
| | | | - Steve A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Echo N Fallon
- Banner University Medical Center-Tucson, Tucson, Arizona, USA
| | - Kevin Yee
- Banner University Medical Center-Tucson, Tucson, Arizona, USA
| | - Justin Kaye
- University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Stuart A Scott
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jason Karnes
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | | | - Jorge Duconge
- University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
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10
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Roche-Lima A, Roman-Santiago A, Feliu-Maldonado R, Rodriguez-Maldonado J, Nieves-Rodriguez BG, Carrasquillo-Carrion K, Ramos CM, da Luz Sant'Ana I, Massey SE, Duconge J. Machine Learning Algorithm for Predicting Warfarin Dose in Caribbean Hispanics Using Pharmacogenetic Data. Front Pharmacol 2020; 10:1550. [PMID: 32038238 PMCID: PMC6987072 DOI: 10.3389/fphar.2019.01550] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Despite some previous examples of successful application to the field of pharmacogenomics, the utility of machine learning (ML) techniques for warfarin dose predictions in Caribbean Hispanic patients has yet to be fully evaluated. This study compares seven ML methods to predict warfarin dosing in Caribbean Hispanics. This is a secondary analysis of genetic and non-genetic clinical data from 190 cardiovascular Hispanic patients. Seven ML algorithms were applied to the data. Data was divided into 80 and 20% to be used as training and test sets. ML algorithms were trained with the training set to obtain the models. Model performance was determined by computing the corresponding mean absolute error (MAE) and % patients whose predicted optimal dose were within ±20% of the actual stabilization dose, and then compared between groups of patients with “normal” (i.e., > 21 but <49 mg/week), low (i.e., ≤21 mg/week, “sensitive”), and high (i.e., ≥49 mg/week, “resistant”) dose requirements. Random forest regression (RFR) significantly outperform all other methods, with a MAE of 4.73 mg/week and 80.56% of cases within ±20% of the actual stabilization dose. Among those with “normal” dose requirements, RFR performance is also better than the rest of models (MAE = 2.91 mg/week). In the “sensitive” group, support vector regression (SVR) shows superiority over the others with lower MAE of 4.79 mg/week. Finally, multivariate adaptive splines (MARS) shows the best performance in the resistant group (MAE = 7.22 mg/week) and 66.7% of predictions within ±20%. Models generated by using RFR, MARS, and SVR algorithms showed significantly better predictions of weekly warfarin dosing in the studied cohorts than other algorithms. Better performance of the ML models for patients with “normal,” “sensitive,” and “resistant” to warfarin were obtained when compared to other populations and previous statistical models.
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Affiliation(s)
- Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities (CCRHH), University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Adalis Roman-Santiago
- Pharmaceutical Sciences Department, School of Pharmacy, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Roberto Feliu-Maldonado
- Center for Collaborative Research in Health Disparities (CCRHH), University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Jovaniel Rodriguez-Maldonado
- Center for Collaborative Research in Health Disparities (CCRHH), University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Brenda G Nieves-Rodriguez
- Center for Collaborative Research in Health Disparities (CCRHH), University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Kelvin Carrasquillo-Carrion
- Center for Collaborative Research in Health Disparities (CCRHH), University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Carla M Ramos
- Department of Biology, College of Natural Sciences, University of Puerto Rico Rio Piedras Campus, San Juan, Puerto Rico
| | - Istoni da Luz Sant'Ana
- Department of Biostatistics and Epidemiology, School of Public Health, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Steven E Massey
- Department of Biology, College of Natural Sciences, University of Puerto Rico Rio Piedras Campus, San Juan, Puerto Rico
| | - Jorge Duconge
- Pharmaceutical Sciences Department, School of Pharmacy, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
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11
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Prospective validation of the International Warfarin Pharmacogenetics Consortium algorithm in high-risk elderly people (VIALE study). THE PHARMACOGENOMICS JOURNAL 2019; 20:451-461. [DOI: 10.1038/s41397-019-0129-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 01/10/2023]
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12
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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13
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Claudio-Campos K, Moneró-Paredes M, Hernández E, Renta J, Duconge J. Low-frequency variants at the CYP2C9 locus among Puerto Rican patients on warfarin: in silico predictions of functionality and conservation. Pharmacogenomics 2019; 20:891-902. [PMID: 31453773 DOI: 10.2217/pgs-2019-0051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Perform in silico predictions of functional consequences of CYP2C9 variants identified by next-generation sequencing in Puerto Ricans. Methods: Identified low-frequency CYP2C9 variants (minor allele frequencies <2%) were evaluated using the Combined Annotation-Dependent Depletion (CADD v1.3) tools and molecular modeling/docking analysis to predict impact on CYP2C9 activity. Results: CYP2C9*5,*8,*9,*11,*12,*21 and a novel *61 induce conformational changes that affect the binding site of S-warfarin. Most of these deleterious variants occur at higher frequency among individuals with large African ancestry. Conclusion: The unfavorable distance of S-warfarin from heme group, and low-binding interactions due to these CYP2C9 variants, suggest major complications during warfarin therapy. This study contributes to the field by predicting functional alterations of rare CYP2C9 variants for the first time in Hispanics.
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Affiliation(s)
- Karla Claudio-Campos
- Department of Pharmacotherapy & Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610-0486, USA
| | - Mariangeli Moneró-Paredes
- Department of Pharmacology & Toxicology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067, USA
| | - Eliud Hernández
- Department of Pharmaceutical Sciences, Medical Sciences Campus, School of Pharmacy, University of Puerto Rico, San Juan, PR 00936-5067, USA
| | - Jessicca Renta
- Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067, USA
| | - Jorge Duconge
- Department of Pharmaceutical Sciences, Medical Sciences Campus, School of Pharmacy, University of Puerto Rico, San Juan, PR 00936-5067, USA
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15
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Claudio-Campos KI, González-Santiago P, Renta JY, Rodríguez J, Carrasquillo K, Gaedigk A, Roche A, Ducongé J. CYP2C9*61, a rare missense variant identified in a Puerto Rican patient with low warfarin dose requirements. Pharmacogenomics 2018; 20:3-8. [PMID: 30518301 DOI: 10.2217/pgs-2018-0143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Warfarin continues to be the mainstay therapy for preventing thrombus formation. Although pharmacogenetic algorithms have shown higher predictability of the optimal warfarin dose and lower occurrence of bleeding episodes, they often do not include ethno-specific genetic variants relevant to non-Europeans. This case report describes a rare missense variant at exon 9 of CYP2C9 (rs202201137; c.1370A>G transition; p.Asn457Ser) found in a Puerto Rican patient with low warfarin dose requirements (3 mg/day). The haplotype characterized by two amino acid changes, Asn457Ser and Arg144Cys (rs1799853; c.430C>T), has been designated CYP2C9*61 by the Pharmacogene Variation Consortium. According to prediction scores assessed with the Combined Annotation Dependent Depletion tool, CYP2C9*61 (p.Asn457Ser) was classified as nondeleterious, therefore its impact on CYP2C9 enzymatic activity cannot be postulated.
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Affiliation(s)
- Karla I Claudio-Campos
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL 36611, USA
| | - Pablo González-Santiago
- Department of Pharmacology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936, Puerto Rico
| | - Jessica Y Renta
- Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936, Puerto Rico
| | - Jovaniel Rodríguez
- Department of Chemistry, Rio Piedras Campus, University of Puerto Rico, San Juan, PR 00931, Puerto Rico
| | - Kelvin Carrasquillo
- Research Centers for Minorities Institutions (RCMI) - Integrated Informatics Services University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00936, Puerto Rico
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Abiel Roche
- Research Centers for Minorities Institutions (RCMI) - Integrated Informatics Services University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00936, Puerto Rico
| | - Jorge Ducongé
- Department of Pharmaceutical Sciences, School of Pharmacy, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936, Puerto Rico
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Galvez JM, Restrepo CM, Contreras NC, Alvarado C, Calderón-Ospina CA, Peña N, Cifuentes RA, Duarte D, Laissue P, Fonseca DJ. Creating and validating a warfarin pharmacogenetic dosing algorithm for Colombian patients. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2018; 11:169-178. [PMID: 30410385 PMCID: PMC6198877 DOI: 10.2147/pgpm.s170515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Purpose Warfarin is an oral anticoagulant associated with adverse reaction to drugs due to wide inter- and intra-individual dosage variability. Warfarin dosage has been related to non-genetic and genetic factors. CYP2C9 and VKORC1 gene polymorphisms affect warfarin metabolism and dosage. Due to the central role of populations’ ethnical and genetic origin on warfarin dosage variability, novel algorithms for Latin American subgroups are necessary to establish safe anticoagulation therapy. Patients and methods We genotyped CYP2C9*2 (c.430C > T), CYP2C9*3 (c.1075A > C), CYP4F2 (c.1297G > A), and VKORC1 (−1639 G > A) polymorphisms in 152 Colombian patients who received warfarin. We evaluated the impact on the variability of patients’ warfarin dose requirements. Multiple linear regression analysis, using genetic and non-genetic variables, was used for creating an algorithm for optimal warfarin maintenance dose. Results Median weekly prescribed warfarin dosage was significantly lower in patients having the VKORC1-1639 AA genotype and poor CYP2C9*2/*2,*2/*3 metabolizers than their wild-type counterparts. We found a 2.3-fold increase in mean dose for normal sensitivity patients (wild-type VKORC1/CYP2C9 genotypes) compared to the other groups (moderate and high sensitivity); 31.5% of the patients in our study group had warfarin sensitivity-related genotypes. The estimated regression equation accounted for 44.4% of overall variability in regard to warfarin maintenance dose. The algorithm was validated, giving 45.9% correlation (R2=0.459). Conclusion Our results describe and validate the first algorithm for predicting warfarin maintenance in a Colombian mestizo population and have contributed toward the understanding of pharmacogenetics in a Latin American population subgroup.
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Affiliation(s)
- Jubby Marcela Galvez
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Carlos Martin Restrepo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Nora Constanza Contreras
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Clara Alvarado
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Carlos-Alberto Calderón-Ospina
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Nidia Peña
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Ricardo A Cifuentes
- Area of Basic Sciences, College of Medicine, Universidad Militar Nueva Granada, Bogotá, Colombia
| | - Daniela Duarte
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Paul Laissue
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Dora Janeth Fonseca
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
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Soares-Souza G, Borda V, Kehdy F, Tarazona-Santos E. Admixture, Genetics and Complex Diseases in Latin Americans and US Hispanics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0151-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Duconge J, Ruaño G. Preventing the exacerbation of health disparities by iatrogenic pharmacogenomic applications: lessons from warfarin. Pharmacogenomics 2018; 19:875-881. [PMID: 29898627 DOI: 10.2217/pgs-2018-0055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jorge Duconge
- Pharmaceutical Sciences Department, School of Pharmacy, University of Puerto Rico Medical Sciences Campus, PO Box 365067, San Juan, PR 00936, USA
| | - Gualberto Ruaño
- Institute of Living at Hartford Hospital, Hartford, CT 06102, USA
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19
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Tavares LC, Marcatto LR, Santos PCJL. Genotype-guided warfarin therapy: current status. Pharmacogenomics 2018; 19:667-685. [PMID: 29701078 DOI: 10.2217/pgs-2017-0207] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Warfarin pharmacogenomics has been an extensively studied field in the last decades as it is focused on personalized therapy to overcome the wide interpatient warfarin response variability and decrease the risk of side effects. In this expert review, besides briefly summarizing the current knowledge about warfarin pharmacogenetics, we also present an overview of recent studies that aimed to assess the efficacy, safety and economic issues related to genotype-based dosing algorithms used to guide warfarin therapy, including randomized and controlled clinical trials, meta-analyses and cost-effectiveness studies. To date, the findings still present disparities, mostly because of standard limitations. Thus, further studies should be encouraged to try to demonstrate the benefits of the application of warfarin pharmacogenomic dosing algorithms in clinical practice.
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Affiliation(s)
- Letícia C Tavares
- Laboratory of Genetics & Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, SP 05403-900, Brazil
| | - Leiliane R Marcatto
- Laboratory of Genetics & Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, SP 05403-900, Brazil
| | - Paulo C J L Santos
- Department of Pharmacology, Universidade Federal de Sao Paulo UNIFESP, SP 04044-020, Brazil
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20
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Suarez-Kurtz G, Parra EJ. Population Diversity in Pharmacogenetics: A Latin American Perspective. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:133-154. [PMID: 29801573 DOI: 10.1016/bs.apha.2018.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pharmacogenetics/pharmacogenomics (PGx) relies on human genetic diversity. In this review we initially examine the PGx implications of human demographic history and genetic diversity, and highlight results from recent studies on the worldwide distribution of common and rare variants in pharmacogenes. The abundance of rare variants implies that a substantial effort will be required to identify their putative functional effects and to develop reliable algorithms for PGx-guided prescription. Furthermore, variants in all pharmacogenes relevant to a drug treatment must be considered. This implies a shift of the current paradigm of PGx-informed prescription based on genotyping a few common variants in selected genes toward comprehensive sequencing approaches. The following sections deal with the impact of population admixture on PGx diversity focusing on Latin America, where a kaleidoscopic combination of individual proportions of Native American, European, and sub-Saharan African ancestries prevails. We illustrate this diversity by contrasting Brazil and Mexico, the two most populous countries in Latin America, and show that population average admixture proportions are not predictive of the corresponding proportions at the individual level. As a consequence of admixture, the genetic differentiation of common pharmacogenetic variants in Latin Americans is much attenuated in comparison to their most relevant ancestral populations. Finally, we review data for tacrolimus and warfarin to illustrate the opportunities and challenges presented by Latin American populations for PGx studies and clinical implementation.
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Affiliation(s)
- Guilherme Suarez-Kurtz
- Instituto Nacional de Câncer and Rede Nacional de Farmacogenética, Rio de Janeiro, Brazil.
| | - Esteban J Parra
- University of Toronto at Mississauga, Mississauga, ON, Canada
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21
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Shah RR, Gaedigk A. Precision medicine: does ethnicity information complement genotype-based prescribing decisions? Ther Adv Drug Saf 2018; 9:45-62. [PMID: 29318005 PMCID: PMC5753996 DOI: 10.1177/2042098617743393] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022] Open
Abstract
Inter-ethnic differences in drug response are all too well known. These are underpinned by a number of factors, including pharmacogenetic differences across various ethnic populations. Precision medicine relies on genotype-based prescribing decisions with the aim of maximizing efficacy and mitigating the risks. When there is no access to genotyping tests, ethnicity is frequently regarded as a proxy of the patient's probable genotype on the basis of overall population-based frequency of genetic variations in the ethnic group the patient belongs to, with some variations being ethnicity-specific. However, ever-increasing transcontinental migration of populations and the resulting admixing of populations have undermined the utility of self-identified ethnicity in predicting the genetic ancestry, and therefore the genotype, of the patient. An example of the relevance of genetic ancestry of a patient is the inadequate performance of European-derived pharmacogenetic dosing algorithms of warfarin in African Americans, Brazilians and Caribbean Hispanics. Consequently, genotyping a patient potentially requires testing for all known clinically actionable variants that the patient may harbour, and new variants that are likely to be identified using state-of the art next-generation sequencing-based methods. Furthermore, self-identified ethnicity is associated with a number of ethnicity-related attributes and non-genetic factors that potentially influence the risk of phenoconversion (genotype-phenotype discordance), which may adversely impact the success of genotype-based prescribing decisions. Therefore, while genotype-based prescribing decisions are important in implementing precision medicine, ethnicity should not be disregarded.
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Affiliation(s)
- Rashmi R. Shah
- Pharmaceutical Consultant, 8 Birchdale, Gerrards Cross, Buckinghamshire, SL9 7JA, UK
| | - Andrea Gaedigk
- Director, Pharmacogenetics Core Laboratory, Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy-Kansas City, Kansas City, MO and School of Medicine, University of Missouri-Kansas City, MO, USA
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22
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Kaye JB, Schultz LE, Steiner HE, Kittles RA, Cavallari LH, Karnes JH. Warfarin Pharmacogenomics in Diverse Populations. Pharmacotherapy 2017; 37:1150-1163. [PMID: 28672100 DOI: 10.1002/phar.1982] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genotype-guided warfarin dosing algorithms are a rational approach to optimize warfarin dosing and potentially reduce adverse drug events. Diverse populations, such as African Americans and Latinos, have greater variability in warfarin dose requirements and are at greater risk for experiencing warfarin-related adverse events compared with individuals of European ancestry. Although these data suggest that patients of diverse populations may benefit from improved warfarin dose estimation, the vast majority of literature on genotype-guided warfarin dosing, including data from prospective randomized trials, is in populations of European ancestry. Despite differing frequencies of variants by race/ethnicity, most evidence in diverse populations evaluates variants that are most common in populations of European ancestry. Algorithms that do not include variants important across race/ethnic groups are unlikely to benefit diverse populations. In some race/ethnic groups, development of race-specific or admixture-based algorithms may facilitate improved genotype-guided warfarin dosing algorithms above and beyond that seen in individuals of European ancestry. These observations should be considered in the interpretation of literature evaluating the clinical utility of genotype-guided warfarin dosing. Careful consideration of race/ethnicity and additional evidence focused on improving warfarin dosing algorithms across race/ethnic groups will be necessary for successful clinical implementation of warfarin pharmacogenomics. The evidence for warfarin pharmacogenomics has a broad significance for pharmacogenomic testing, emphasizing the consideration of race/ethnicity in discovery of gene-drug pairs and development of clinical recommendations for pharmacogenetic testing.
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Affiliation(s)
- Justin B Kaye
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Lauren E Schultz
- Department of Pharmacology and Toxicology, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Heidi E Steiner
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Rick A Kittles
- Department of Public Health, University of Arizona College of Medicine, Tucson, Arizona.,Department of Surgery, University of Arizona College of Medicine, Tucson, Arizona.,Center for Applied Genetics and Genomic Medicine, University of Arizona College of Medicine, Tucson, Arizona
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona.,Center for Applied Genetics and Genomic Medicine, University of Arizona College of Medicine, Tucson, Arizona.,Sarver Heart Center, University of Arizona College of Medicine, Tucson, Arizona
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23
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Martes-Martinez C, Méndez-Sepúlveda C, Millán-Molina J, French-Kim M, Marín-Centeno H, Rivera-Miranda GC, Hernández-Muñoz JJ, Duconge-Soler J. Cost-Utility Study of Warfarin Genotyping in the VACHS Affiliated Anticoagulation Clinic of Puerto Rico. PUERTO RICO HEALTH SCIENCES JOURNAL 2017; 36:165-172. [PMID: 28915306 PMCID: PMC5993426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To evaluate the cost-utility of the pharmacogenetic-guided dosing of warfarin (PGx), when compared to the current dosing strategy. METHODS A Markov model was developed to assess the impact of the genotypingguided warfarin dosing in a hypothetical cohort of patients. The model was based on the percentage of time patients spent within the therapeutic international normalized ratio (INR) range (PTTR). PTTR estimates and genotype distribution were derived from a cohort of patients (n = 206) treated in the Veteran Affairs Caribbean Healthcare System (VACHS) and from results of other research study. Costs, utilities and event probability data were obtained from the literature. Probabilistic and one-way sensitivity analyses were performed to explore the range of plausible results. Willingness to pay was established at $50,000 per Quality Adjusted Life Year (QALY) gained. RESULTS According to our model, the PGx strategy showed a QALY increase of 0.0021, with an increase in total cost of $272. This corresponds to an incremental cost-utility ratio (ICUR) of $127,501, ranging from $95,690 to $148,611. One-way sensitivity analysis revealed that the ICURs were more sensitive to the cost of genotyping and the effect of genotyping on the PTTR. CONCLUSION Our model suggests that the warfarin PGx was not superior to the standard of care dosing strategy in terms of cost-utility.
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Affiliation(s)
- Carlos Martes-Martinez
- Pharmacy Practice Department, School of Pharmacy, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
| | - Cristian Méndez-Sepúlveda
- Pharmacy Practice Department, School of Pharmacy, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
| | - Joel Millán-Molina
- Pharmacy Practice Department, School of Pharmacy, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
| | | | - Heriberto Marín-Centeno
- Health Services Administration Department, School of Public Health, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | | | - José J Hernández-Muñoz
- Pharmacy Practice Department, School of Pharmacy, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico; Pharmaceutical Sciences Department, College of Pharmacy, Texas A&M University, College Station, TX
| | - Jorge Duconge-Soler
- Pharmaceutical Sciences Department, School of Pharmacy, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
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Claudio-Campos K, Labastida A, Ramos A, Gaedigk A, Renta-Torres J, Padilla D, Rivera-Miranda G, Scott SA, Ruaño G, Cadilla CL, Duconge-Soler J. Warfarin Anticoagulation Therapy in Caribbean Hispanics of Puerto Rico: A Candidate Gene Association Study. Front Pharmacol 2017; 8:347. [PMID: 28638342 PMCID: PMC5461284 DOI: 10.3389/fphar.2017.00347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/14/2022] Open
Abstract
Existing algorithms account for ~50% of observed variance in warfarin dose requirements after including common polymorphisms. However, they do not perform as well in populations other than Caucasians, in part because some ethno-specific genetic variants are overlooked. The objective of the present study was to identify genetic polymorphisms that can explain variability in warfarin dose requirements among Caribbean Hispanics of Puerto Rico. Next-Generation Sequencing of candidate genes CYP2C9 and VKORC1 and genotyping by DMET® Plus Assay of cardiovascular patients were performed. We also aimed at characterizing the genomic structure and admixture pattern of this study cohort. Our study used the Extreme Discordant Phenotype approach to perform a case-control association analysis. The CYP2C9 variant rs2860905, which was found in all the major haplotypes occurring in the Puerto Rican population, showed stronger association with warfarin sensitivity (<4 mg/day) than common variants CYP2C9*2 and CYP2C9*3. Although, CYP2C9*2 and CYP2C9*3 are separately contained within two of the haplotypes, 10 subjects with the sensitive phenotype were carriers of only the CYP2C9 rs2860905 variant. Other polymorphisms in CES2 and ABCB1 were found to be associated with warfarin resistance. Incorporation of rs2860905 in a regression model (R2 = 0.63, MSE = 0.37) that also includes additional genetics (i.e., VKORC1-1639 G>A; CYP2C9 rs1856908; ABCB1 c.IVS9-44A>G/ rs10276036; CES2 c.269-965A>G/ rs4783745) and non-genetic factors (i.e., hypertension, diabetes and age) showed better prediction of warfarin dose requirements than CYP2C9*2 and CYP2C9*3 combined (partial R2 = 0.132 vs. 0.023 and 0.007, respectively, p < 0.001). The genetic background of Puerto Ricans in the study cohort showed a tri-hybrid admixture pattern, with a slightly higher than expected contribution of Native American ancestry (25%). The genomic diversity of Puerto Ricans is highlighted by the presence of four different major haplotype blocks in the CYP2C9 locus. Although, our findings need further replication, this study contributes to the field by identifying novel genetic variants that increase predictability of stable warfarin dosing among Caribbean Hispanics.
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Affiliation(s)
- Karla Claudio-Campos
- Department of Pharmacology and Toxicology, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Aurora Labastida
- Independent Researcher, Primera Cerrada de Camino al Amalillo 4Mexico City, Mexico
| | - Alga Ramos
- Miami VA Healthcare System, Health System Administration Pharmacy, Clinical ServicesMiami, FL, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, United States
| | - Jessicca Renta-Torres
- Department of Biochemistry, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Dariana Padilla
- Department of Biology, University of Puerto Rico at Rio PiedrasSan Juan, PR, United States
| | - Giselle Rivera-Miranda
- Veterans Affairs Caribbean Healthcare Systems, Pharmacy ServiceSan Juan, PR, United States
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew York, NY, United States
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized MedicineNew York, NY, United States
| | | | - Carmen L. Cadilla
- Department of Biochemistry, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Jorge Duconge-Soler
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto RicoSan Juan, PR, United States
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25
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Hernandez-Suarez DF, Claudio-Campos K, Mirabal-Arroyo JE, Torres-Hernández BA, López-Candales A, Melin K, Duconge J. Potential of a Pharmacogenetic-Guided Algorithm to Predict Optimal Warfarin Dosing in a High-Risk Hispanic Patient: Role of a Novel NQO1*2 Polymorphism. J Investig Med High Impact Case Rep 2016; 4:2324709616682049. [PMID: 28210634 PMCID: PMC5298566 DOI: 10.1177/2324709616682049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023] Open
Abstract
Deep abdominal vein thrombosis is extremely rare among thrombotic events secondary to the use of contraceptives. A case to illustrate the clinical utility of ethno-specific pharmacogenetic testing in warfarin management of a Hispanic patient is reported. A 37-year-old Hispanic Puerto Rican, non-gravid female with past medical history of abnormal uterine bleeding on hormonal contraceptive therapy was evaluated for abdominal pain. Physical exam was remarkable for unspecific diffuse abdominal tenderness, and general initial laboratory results-including coagulation parameters-were unremarkable. A contrast-enhanced computed tomography showed a massive thrombosis of the main portal, splenic, and superior mesenteric veins. On admission the patient was started on oral anticoagulation therapy with warfarin at 5 mg/day and low-molecular-weight heparin. The prediction of an effective warfarin dose of 7.5 mg/day, estimated by using a recently developed pharmacogenetic-guided algorithm for Caribbean Hispanics, coincided with the actual patient's warfarin dose to reach the international normalized ratio target. We speculate that the slow rise in patient's international normalized ratio observed on the initiation of warfarin therapy, the resulting high risk for thromboembolic events, and the required warfarin dose of 7.5 mg/day are attributable in some part to the presence of the NQO1*2 (g.559C>T, p.P187S) polymorphism, which seems to be significantly associated with resistance to warfarin in Hispanics. By adding genotyping results of this novel variant, the predictive model can inform clinicians better about the optimal warfarin dose in Caribbean Hispanics. The results highlight the potential for pharmacogenetic testing of warfarin to improve patient care.
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Affiliation(s)
| | | | | | - Bianca A Torres-Hernández
- University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA; University of Puerto Rico Humacao Campus, Humacao, PR, USA
| | | | - Kyle Melin
- University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
| | - Jorge Duconge
- University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
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Duconge J, Ruaño G. Admixture and ethno-specific alleles: missing links for global pharmacogenomics. Pharmacogenomics 2016; 17:1479-82. [DOI: 10.2217/pgs-2016-0115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Jorge Duconge
- School of Pharmacy, University of Puerto Rico Medical Sciences Campus, PO Box 365067, San Juan, PR 00936, USA
| | - Gualberto Ruaño
- Pharmaceutical Sciences Department, Genomas Inc., Hartford, CT 06102, USA
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